June 2021 - phenixbb - phenix-online.org

C-C sugar linkage in real-space refinement
by Kevin Jude 15 Jun '21

15 Jun '21

I'm trying to refine a cryoEM structure that contains some MAN/C1-TRP/CD1 glycosylations. I've done this successfully in crystallographic reciprocal space refinement, using cif files to define the MAN geometry and the MAN-TRP linkage, plus adding LINK instructions to the pdb file. In this cryoEM structure, though, using the same .cif definition files and similar LINK instruction, the bond is still not defined in the .geo file and instead it's treated as a nonbonded interaction, kicking the mannose away from the indole side chain. The NAG-ASN linkages in the cryoEM structure are fine. Do I need to do anything differently to define these linkages in Real Space Refine compared to phenix.refine? -- Kevin Jude, PhD (he/him/his) Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305 Phone: (650) 723-6431

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Turn off side chain optimizations in phenix real space refine?
by Oliver Clarke 12 Jun '21

12 Jun '21

Hi, Is there any way to turn off rotamer fitting/side chain optimization in phenix.real_space_refine? Sometimes it seems to do more harm than good, and repositions sidechains completely out of the density, but I couldn't find how to switch it off. Cheers Oli

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General interest: the history of the European Crystallography Schools
by John R Helliwell 11 Jun '21

11 Jun '21

Dear Colleagues, Th history of the European Crystallography Schools, initiated by Italian colleagues (ECS1 was held in Pavia), is described here at the ECA’s website:- https://ecanews.org/european-crystallography-school/ Several of these previous Schools’ details, but not all as yet, can be found here:- https://ecsx.ecanews.org/ ie replacing the x by the number. The current one ‘Budapest’ being 6. (In each the ECA website is mirrored to the local host organising team.) Greetings, John Emeritus Professor John R Helliwell DSc ECA Past President 2007 to 2010

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European Crystallography School ECS6
by John R Helliwell 11 Jun '21

11 Jun '21

Dear Colleagues, I commend to you the European Crystallography School ECS6. Full details are here:- https://akcongress.com/ecs6/ Best wishes, John Emeritus Professor John R Helliwell DSc

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Restraints for small molecules in macromolecular crystal structures
by Marie Elizabeth Fraser 11 Jun '21

11 Jun '21

Hello, The parameters we use as restraints for small molecules in complex with macromolecules have improved greatly, but we still get complaints when submitting to the Protein Data Bank. We use grade to obtain restraints for these small molecules, but when we submit to the PDB, some of their restraints do not match. I am not clear where the PDB gets these restraints, but we edit our file to match the values sent and finish the refinement. What do others do? As well, PHENIX and COOT aren’t accessing the same library for restraints. Is this due to how I’ve installed ccp4 (for COOT) and PHENIX? The small molecule whose restraints I currently need is ADP metavanadate (AD9), which grade won’t accept because of the vanadium, so I used elbow to calculate restraints. Thank you, Marie

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Associate Researcher Position in the KU Protein Structure Laboratory
by Lovell, Scott W 09 Jun '21

09 Jun '21

The Protein Structure Laboratory (PSL) at the University of Kansas (KU) is seeking a full-time Associate Researcher to assist with various structural biology projects. As a core laboratory, the PSL collaborates with a diverse range of investigators to obtain structures of their proteins of interest using X-ray crystallography and delivers dozens of structures annually. Additionally, the PSL manages the structural biology efforts for extramurally funded research projects particularly aimed at inhibitor development. For a full description of the position and to apply, GO TO: https://employment.ku.edu/associate-researcher/19212br Regards, Scott __________________________________________________ Scott Lovell Ph.D., Director Protein Structure and X-Ray Crystallography Laboratory University of Kansas Del Shankel Structural Biology Center 2034 Becker Drive Lawrence, KS 66047 Office: SBC 1015 email: swlovell(a)ku.edu<mailto:[email protected]> phone: 785-864-3772 fax: 785-864-8141 __________________________________________________

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Postdoctoral Scholarship Opportunity in the Lane group (PBIO) CFEL/DESY, Hamburg, Germany
by TJ Lane 08 Jun '21

08 Jun '21

Uncovering protein dynamics: developing statistical crystallography Postdoctoral Scholarship Cluster of Excellence: Advanced Imaging of Matter Center for Free Electron Laser Science (CFEL), Hamburg, Germany Protein motion is at the heart of life, but remains challenging to witness firsthand. Proteins move to reading and copying DNA, convert sunlight into chemical energy, and transmit signals between cells, yet our ability to image these functions is limited by the technology we have to image protein dynamics. A new opportunity to meet this challenge is emerging, however, as crystallographic methods advance. We can now collect data from thousands to millions of crystals of the same protein, and it is clear no two crystals are identical. Thus, analyzing their distribution may reveal protein structural fluctuations directly. Can we develop a statistical crystallography to turn these large datasets into knowledge about protein dynamics? Can we use statistical analysis of crystal-to-crystal variation to separate signal from noise in time resolved experiments, revealing protein motion induced by mixing with a ligand or excitation with a pump laser? We seek a computational scientist who will answer these questions. As the ideal candidate, you will have the following key attributes: * A doctoral degree in physics, biophysics, chemistry, applied mathematics or a related field * Working knowledge of macromolecular crystallographic methods and software * A track record of scientific computing and programming * The ability to drive your work independently and show initiative And you will be excited to take on the following responsibilities: * Mathematical modeling of protein dynamics and protein crystal diffraction data * Interpretation and analysis of experimental results * Open-source development to make your insights available to the broader scientific community * Presenting your work in written and oral form to the scientific community * Helping to foster an environment conductive to collaboration, learning, growth, and fun Available immediately is a two-year contract with a competitive salary and the opportunity to work and live in the beautiful and vibrant city of Hamburg, Germany. The group is housed at the Center for Free Electron Laser Science on the vibrant DESY campus (Luruper Chaussee 149, 22761 Hamburg, Germany). This position is funded through the Advanced Imaging of Matter Cluster of Excellence (https://www.cui-advanced.uni-hamburg.de/en.html). The successful candidate will become a fellow of the cluster and have access to career support, training opportunities, and an engaging scientific network via the cluster. The candidate will have additional technical and mentorship support from partners Andrea Thorne, Arwen Pearson, and Nicholas Pearce and their groups during the course of the project. We are an equal opportunity employer. Women and minorities are encouraged to apply and handicapped persons will be preferred given equal qualifications. Application deadline: 17 June 2021 Applications should include a cover letter, a tabular curriculum vitae, and copies of degree certificate(s). Please send applications by email to: < thomas.lane(a)desy.de> For more details, write directly to TJ Lane: <thomas.lane(a)desy.de> Cross-Posting on the AIM Cluster of Excellence page (funding source for this project): https://www.uni-hamburg.de/stellenangebote/ausschreibung.html?jobID=4c3ff9d…

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Quick calculation of mean ADP
by Martin Malý 08 Jun '21

08 Jun '21

Dear mailing list members, I would like to calculate the mean ADP of a structure model (PDB) from a Python script using tools in CCTBX/PHENIX. I tried to find out how and dig it from Python source code but I have been unsuccessful yet. Please, how to do it (in Python)? Although It is quite easy to calculate it in on my own directly from PDB for isotropic ADPs, the situation can be a bit complicated for anisotropic ADPs... Thank you. Best regards, Martin Mal ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 04 Jun '21

04 Jun '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 JUN 2021. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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